Abstract

Recent work shows that the inhibition of the SOS stress response in Escherichia coli reduces the development of resistance to the antibiotics ciprofloxacin and rifampicin.
This finding may help in the battle against the rise of resistance to antimicrobial
drugs.

Minireview

Bacterial resistance to antimicrobial drugs is currently receiving much publicity
and political attention. The cost to health services around the world is counted in
billions of dollars; an increase in morbidity and mortality are the costs to those
infected. The problem is getting worse and treatment options for combating bacteria
resistant to multiple drugs are narrowing. Unless something is done, we may well return
to the horrors of the pre-antibiotic era. In a recent article, Cirz and colleagues
[1] report the interesting finding that the rate of resistance to some drugs in Escherichia coli can be greatly reduced by interfering with a bacterial stress response. This article
sets the work by Cirz et al. [1] in the general context of antimicrobial drug resistance and discusses whether this
new finding could be helpful in the battle against the rise of drug-resistant bacteria.

Are 'mutation-busting' drugs the answer to the problem of drug resistance?

Resistance to antimicrobials occurs in four main ways (Figure 1). The first possible mechanism is the mutation of the drug's target; a classic example
of this is the mutation of gyrA, encoding the essential DNA gyrase A subunit, the major target of quinolones such
as ciprofloxacin in E. coli [2]. A second mechanism is a bypass of the drug's target by the acquisition of a similar
but insensitive target protein. A good example here would be the acquisition of a
plasmid-borne dihydrofolate reductase (DHFR) insensitive to trimethoprim; the acquired
DHFR compensates for the inhibition of the host's DHFR in the presence of trimethoprim
and is the predominant cause of resistance to this antimicrobial drug in E. coli [3]. A third mechanism is the enzymatic degradation or modification of the drug; a well-known
example is the destruction of β-lactam antibiotics by plasmid-mediated TEM β-lactamase,
which accounts for around 90% of all ampicillin resistance in E. coli [4]. And fourth, resistance can be caused by a nonspecific reduced permeability to antimicrobial
drugs. This is typically caused by reduced production of porins, the protein channels
that allow antimicrobials through the outer bacterial membrane, and/or an increased
production of drug-efflux pumps, which remove drugs from both cytoplasm and periplasm
[5]. These two events are often coordinated, for example through the Mar regulon in E. coli, which - when constitutively activated by mutation - leads to resistance to multiple
antimicrobial drugs [6].

Figure 1. Antimicrobial drug-resistance mechanisms. A typical Gram-negative bacterial cell envelope
is shown, consisting of the outer membrane, the peptidoglycan cell wall, the periplasm,
which contains enzymes required to synthesize the cell wall, and the cytoplasmic membrane.
(a) The entry point and targets of antimicrobial drugs in a non-resistant bacterium. Drugs
enter the periplasm through porins in the outer membrane, and some drugs exert their
effect in the periplasm; for example, ampicillin and the other β-lactams interfere
with the synthesis of the cell wall. Other drugs cross the cytoplasmic membrane and
inhibit cytoplasmic targets. (b) Possible resistance mechanisms: (1) Mutation of a target so that it is no longer inhibited
by the drug; (2) acquisition, for example on a plasmid, of a novel target that is
not sensitive to the actions of the drug; (3) enzymatic destruction or modification
of the drug either in the cytoplasm, for example, the inactivation of gentamicin by
aminoglycoside-modifying enzymes, or in the periplasm, for example, the destruction
of β-lactams by β-lactamase; (4) reduction of the cytoplasmic, and usually periplasmic,
concentration of the drug through reduction in the expression of porin genes or loss-of-function
mutations in porin genes; (5) removal of drugs from the periplasm or cytoplasm by
efflux pumps. In some cases, drug resistance is due to a combination of these mechanisms.

Mutations are an unavoidable fact of life, but it has long been known that gyrA mutations leading to ciprofloxacin resistance in E. coli occur at a higher frequency than one might expect given E. coli's general rate of mutation [7]. One process that leads to increased mutation in E. coli is the SOS response, which is triggered in response to a wide range of stress conditions.
It is known to cause increased mutation rates, particularly following DNA damage.
The unblocking of stalled replication forks, which are a common and potentially lethal
result of DNA damage, requires the SOS response, for example. The trigger for the
SOS response is the autolytic degradation of the transcriptional repressor/protease
hybrid, LexA, thus derepressing the expression of a group of genes whose products
are responsible for DNA repair and unblocking of stalled replication forks. These
proteins include error-prone DNA polymerases, whose activities lead to the increased
frequency of mutation seen in cells during the SOS response [8].

In their recent article, Cirz et al. [1] postulate that ciprofloxacin induces DNA damage and so instigates the SOS response,
thereby increasing the frequency at which ciprofloxacin-resistant mutants arise in
E. coli. Through a series of in vitro experiments, they confirmed that this is the case, and that mutations in lexA that block the SOS response result in a reduction in the apparent frequency of mutation
to ciprofloxacin resistance in vitro. Another lexA mutant strain had the ciprofloxacin mutation frequency apparently reduced to zero
compared to the wild-type parent, when tested in a murine model of infection [1].

The gyrA mutations caused by ciprofloxacin-mediated induction of the SOS response were all
confirmed as being base substitutions, typical of those seen in the clinic. Cirz et al. [1] postulate, however, that ciprofloxacin also induces some other repair system, which
causes small deletions, as some of the ciprofloxacin-resistant mutants had deletions
of entire triplets in gyrA. Such mutants are not seen clinically, and it is highly likely that they come with
an extreme fitness cost.

The authors found the same pattern of results when looking at the frequency of occurrence
of rifampicin-resistant mutants caused by point mutations in the rpoB gene encoding the beta subunit of RNA polymerase. This is perhaps surprising, because
rifampicin does not cause DNA damage, being an inhibitor of RNA polymerase. Several
antibiotics are, however, known to cause metabolic stress and induce the SOS response
without overtly causing DNA damage; these include for example, the β-lactams [9].

The work of Cirz et al. [1] at least opens up the possibility that inhibitors of the SOS response might represent
drugs that reduce point mutation rates in bacteria, and so reduce the frequency with
which drug-resistant mutations occur. But would this really be of benefit? Taking
the example of quinolone resistance in E. coli, the answer is 'yes and no'. As well as target-site mutations, efflux pump and/or
porin regulatory mutations can cause antimicrobial drug resistance [5], so mutation-busting drugs could be doubly helpful. On the other hand, mutations
are not the only cause of resistance. For example, mobile genetic elements can cause
quinolone resistance in two main ways. First, the insertion of mobile IS elements can derepress efflux-pump gene expression and disrupt porin genes [5]. Second, plasmid-mediated quinolone-resistance determinants are becoming increasingly
common; these encode proteins that bind to the active sites of quinolone targets and
occlude the drugs [10]. Indeed, there are no classes of antimicrobial drug for which point mutations are
the sole reason for the development of resistance. So the best one can say is that
mutation-busting drugs would reduce the development of resistance due to mutation.
They would, however, do nothing to prevent the development of resistance due to mobile
genetic elements. Furthermore, it is likely that by the time they have been developed,
many of the mutations they are designed to stop will already have occurred.

Other approaches to solving the problem of antimicrobial drug resistance

Other strategies for combating antimicrobial drug resistance fall into three main
types. First, simply develop new drugs. The post-genomic era has led to the discovery
of a whole host of essential genes in bacteria whose products might represent targets
for novel antimicrobial drugs. But the exploitation of these targets is proving very
difficult. More useful has been the adaptation of known drug scaffolds so that they
overcome existing resistance mechanisms [11,12]. It is, however, unlikely that permeability-mediated resistance mechanisms of Gram-negative
bacteria will be overcome by these new drug variants, as these resistance mechanisms
affect a broad spectrum of antibiotics [5]. The second approach is to stop using a particular drug and reintroduce it when resistance
levels have fallen. This idea derives from the assumption that resistance mechanisms
come with a fitness cost and that in the absence of selection, resistant strains will
be out-competed by sensitive strains. Recent work has revealed, however, that most
resistance mechanisms impose no significant fitness cost; indeed some may provide
a fitness advantage [13,14], and this may explain why sulfonamide-resistance levels in E. coli did not fall in the UK even 10 years after the use of sulfonamides had been discontinued
[15]. The third strategy is to learn more about the resistance mechanisms themselves.
This area of research is focused on degradative enzymes and efflux pumps. The β-lactamase
inhibitors already used clinically have been most successful but do not inhibit a
large swathe of these enzymes, so more are required [16]; efflux-pump inhibitors exist but are not currently in a clinically useful form [17].

In conclusion, the problem of antimicrobial drug resistance is very real, and is set
to get worse before it gets better. The more we learn about the responses of bacteria
to antimicrobial challenge, and about the fundamental mechanisms of drug resistance
in bacteria, the more likely we are to be able to develop strategies for reducing
the burden of resistance. The availability of large amounts of complete bacterial
genome sequence data, coupled with the development of post-genomic technologies aimed
at comparing gene complements and gene-expression patterns in resistant and non-resistant
bacteria (for example [18,19]), gives us an excellent platform to study resistance mechanisms. So, the dawn of
the post-genomic era may help to delay a return to the pre-antibiotic era. Only time
will tell.

Acknowledgements

I thank the Biotechnology and Biological Research Council, the Medical Research Council,
the Wellcome Trust, the British Society for Antimicrobial Chemotherapy and the Royal
Society for funding.